Abstract：
:A major goal of system biology is the characterization of transcription factors and microRNAs (miRNAs) and the transcriptional programs they regulate. We present Allegro, a method for de-novo discovery of cis-regulatory transcriptional programs through joint analysis of genome-wide expression data and promoter or 3' UTR sequences. The algorithm uses a novel log-likelihood-based, non-parametric model to describe the expression pattern shared by a group of co-regulated genes. We show that Allegro is more accurate and sensitive than existing techniques, and can simultaneously analyze multiple expression datasets with more than 100 conditions. We apply Allegro on datasets from several species and report on the transcriptional modules it uncovers. Our analysis reveals a novel motif over-represented in the promoters of genes highly expressed in murine oocytes, and several new motifs related to fly development. Finally, using stem-cell expression profiles, we identify three miRNA families with pivotal roles in human embryogenesis.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Halperin Y,Linhart C,Ulitsky I,Shamir Rdoi
10.1093/nar/gkn1064subject
Has Abstractpub_date
2009-04-01 00:00:00pages
1566-79issue
5eissn
0305-1048issn
1362-4962pii
gkn1064journal_volume
37pub_type
杂志文章abstract：:Inadequate cellular compartmentalisation of plasmid DNA and antisense oligodeoxynucleotides (ODNs) is generally considered as a major limitation in their use. In this study, an approach combining in situ visual-isation of rhodamine-labelled ODNs and affinity modification of proteins by radiolabelled-alkylating ODN der...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/27.11.2315
更新日期：1999-06-01 00:00:00
abstract：:Elastic network models (ENMs) are valuable and efficient tools for characterizing the collective internal dynamics of proteins based on the knowledge of their native structures. The increasing evidence that the biological functionality of RNAs is often linked to their innate internal motions poses the question of whet...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkv708
更新日期：2015-09-03 00:00:00
abstract：:Nucleic acid double helices are stabilized by hydrogen bonding and stacking forces (a combination of hydrophobic, dispersive and electrostatic forces) of the base pairs in the helix. One would predict the hydrogen bonding contributions to increase and the stacking contributions to decrease as the water activity in the...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkm210
更新日期：2007-01-01 00:00:00
abstract：:The Mouse Genome Database (MGD: http://www.informatics.jax.org) is the primary community data resource for the laboratory mouse. It provides a highly integrated and highly curated system offering a comprehensive view of current knowledge about mouse genes, genetic markers and genomic features as well as the associatio...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkw1040
更新日期：2017-01-04 00:00:00
abstract：:The regions of the polypeptide chain immediately preceding or following an α-helix are known as Nt- and Ct cappings, respectively. Cappings play a central role stabilizing α-helices due to lack of intrahelical hydrogen bonds in the first and last turn. Sequence patterns of amino acid type preferences have been derived...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkr879
更新日期：2012-01-01 00:00:00
abstract：:The Genomes Online Database (GOLD) (https://gold.jgi.doe.gov) is an open online resource, which maintains an up-to-date catalog of genome and metagenome projects in the context of a comprehensive list of associated metadata. Information in GOLD is organized into four levels: Study, Biosample/Organism, Sequencing Proje...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gky977
更新日期：2019-01-08 00:00:00
abstract：:Genome packing in adenovirus has long evaded precise description, since the viral dsDNA molecule condensed by proteins (core) lacks icosahedral order characteristic of the virus protein coating (capsid). We show that useful insights regarding the organization of the core can be inferred from the analysis of spatial di...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkv187
更新日期：2015-04-30 00:00:00
abstract：:A 170bp long BamHI-Sau3A DNA fragment from the actIII-actI intergenic region of the actinorhodin (Act) biosynthetic gene cluster of Streptomyces coelicolor A3(2) contains two promoters directing transcription in a divergent manner. One of them, the actIII promoter, is responsible for the transcription of the actIII ge...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/19.10.2623
更新日期：1991-05-25 00:00:00
abstract：:The intrinsic stiffness of DNA limits its ability to be bent and twisted over short lengths, but such deformations are required for gene regulation. One classic paradigm is DNA looping in the regulation of the Escherichia coli lac operon. Lac repressor protein binds simultaneously to two operator sequences flanking th...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkm419
更新日期：2007-01-01 00:00:00
abstract：:The irradiation of native or unmodified yeast tRNA(Phe) by short wavelength UV light (260 nM) results in an intramolecular crosslink that has been mapped to occur between C48 in the variable loop and U59 in the T loop. Photo-reversibility of the crosslink and the absence of fluorescent photo adducts suggest that the c...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/20.15.4055
更新日期：1992-08-11 00:00:00
abstract：:The translational regulation of ferritin expression currently represents the only well characterized example for eukaryotic translational control by high affinity interactions between a specific cytoplasmic protein, iron regulatory factor [IRF], and an mRNA-binding site, the iron-responsive element [IRE], located in t...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/20.21.5555
更新日期：1992-11-11 00:00:00
abstract：:Acetyl-CoA Carboxylase catalyzes the first committed step in fatty acid synthesis. Escherichia coli acetyl-CoA carboxylase is composed of biotin carboxylase, carboxyltransferase and biotin carboxyl carrier protein functions. The accA and accD genes that code for the alpha- and beta-subunits, respectively, are not in a...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkp1079
更新日期：2010-03-01 00:00:00
abstract：:Active DNA demethylation (ADDM) in mammals occurs via hydroxylation of 5-methylcytosine (5mC) by TET and/or deamination by AID/APOBEC family enzymes. The resulting 5mC derivatives are removed through the base excision repair (BER) pathway. At present, it is unclear how the cell manages to eliminate closely spaced 5mC ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkw059
更新日期：2016-05-05 00:00:00
abstract：:Gene expression profiling has gradually become a routine procedure for disease diagnosis and classification. In the past decade, many computational methods have been proposed, resulting in great improvements on various levels, including feature selection and algorithms for classification and clustering. In this study,...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkt343
更新日期：2013-08-01 00:00:00
abstract：:Existence of some extra-genetic (epigenetic) codes has been postulated since the discovery of the primary genetic code. Evident effects of histone post-translational modifications or DNA methylation over the efficiency and the regulation of DNA processes are supporting this postulation. EMdeCODE is an original algorit...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gks1214
更新日期：2013-02-01 00:00:00
abstract：:Toscana virus (TOSV) is an arthropod-borne human pathogen responsible for seasonal outbreaks of fever and meningoencephalitis in the Mediterranean basin. TOSV is a segmented negative-strand RNA virus (sNSV) that belongs to the genus phlebovirus (family Phenuiviridae, order Bunyavirales), encompassing other important h...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkz838
更新日期：2019-11-18 00:00:00
abstract：:Transcript of the rbpA1 gene in Anabaena variabilis accumulates significantly at low growth temperatures below 28 degreesC. This accumulation was maximal at 16 degreesC. Accumulation of the rbpA1 transcript was completely abolished by rifampicin, but not by chloramphenicol. Photosynthesis was not required for this col...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/26.9.2192
更新日期：1998-05-01 00:00:00
abstract：:The (cytosine-5) DNA methyltransferase M.HhaI causes its target cytosine base to be flipped completely out of the DNA helix upon binding. We have investigated the effects of replacing the target cytosine by other, mismatched bases, including adenine, guanine, thymine and uracil. We find that M.HhaI binds more tightly ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/23.8.1388
更新日期：1995-04-25 00:00:00
abstract：:Ovarian poly (A) + RNA from Xenopus laevis and Xenopus borealis was used to construct two cDNA libraries which were screened for histone sequences. cDNA clones to H4 mRNA were obtained from both species and an H3 cDNA clone from Xenopus laevis. The complete DNA sequences of these clones have been determined and are pr...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/10.12.3769
更新日期：1982-06-25 00:00:00
abstract：:Tubercidin may be directly brominated by reaction with N-bromosuccinimide in DMF to give 5-bromotubercidin, a reversible inhibitor of RNA synthesis. When buffered with potassium acetate the major product is 6-bromotubercidin. 5,6-Dibromotubercidin is formed in minor amounts under both conditions. N-Chlorosuccinimide a...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/8.24.6213
更新日期：1980-12-20 00:00:00
abstract：:Transcription and mRNA export are linked processes. However, the molecular mechanisms of this coordination are not clear. Sus1 (hENY2) participates in this coordination as part of two protein complexes: SAGA, a transcriptional co-activator; TREX-2, which functions in mRNA biogenesis and export. Here, we investigate th...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkt272
更新日期：2013-06-01 00:00:00
abstract：:Gene set enrichment testing can enhance the biological interpretation of ChIP-seq data. Here, we develop a method, ChIP-Enrich, for this analysis which empirically adjusts for gene locus length (the length of the gene body and its surrounding non-coding sequence). Adjustment for gene locus length is necessary because ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gku463
更新日期：2014-07-01 00:00:00
abstract：:Ribonucleotides are misincorporated into replicating DNA due to the similarity of deoxyribonucleotides and ribonucleotides, the high concentration of ribonucleotides in the nucleus and the imperfect accuracy of replicative DNA polymerases in choosing the base with the correct sugar. Embedded ribonucleotides change cer...
journal_title：Nucleic acids research
pub_type： 杂志文章,评审
doi：10.1093/nar/gku773
更新日期：2014-01-01 00:00:00
abstract：:DNA sequences, that control expression of the spliced leader (SL) RNA gene in the parasitic protozoan Leishmania amazonensis, were mapped by block substitution mutagenesis. In the absence of a functional in vitro system for transcription, no promoter elements have yet been identified in this organism. We therefore dev...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/22.11.1959
更新日期：1994-06-11 00:00:00
abstract：:The human gene for plasminogen activator inhibitor type-1 (PAI-1) has been isolated and its promoter region characterized. PAI-1 regulation by glucocorticoids, transforming growth factor-beta (TGF-beta) and the phorbol ester PMA is shown to be exerted at the promoter level. A fragment spanning 805 nucleotides of the 5...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/16.7.2805
更新日期：1988-04-11 00:00:00
abstract：:A linear DNA plasmid, designated pLLE1, has been isolated from a mitochondrial fraction of a strain of Lentinus edodes. pLLE1(11.0 kbp) was sensitive to the 3'----5'-acting exonuclease III and resistant to the 5'----3'-acting lambda exonuclease. It showed no homology with mitochondrial and nuclear genomic DNAs of plas...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/18.6.1395
更新日期：1990-03-25 00:00:00
abstract：:The early DNa products of reverse transcription have been analyzed from reconstructed reactions containing avian myeloblastosis virus 35S RNA . tRNAtrp complex and highly purified reverse transcriptase. We describe conditions for the synthesis of genome-length complementary DNA and two discrete species of plus strand ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/10.3.1009
更新日期：1982-02-11 00:00:00
abstract：:The synthetic DNA fragment (formula, see text) (corresponding to nucleotides 4299-4314 of the phi X DNA sequence) was cloned into either the AmpR gene or the KmR gene of plasmid pACYC 177. The DNA sequence of the KmR gene around the insertion site was determined by nucleotide sequence analysis of the pACYC 177 FnudII ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/9.14.3335
更新日期：1981-07-24 00:00:00
abstract：:Human La protein is an essential factor in the biology of both coding and non-coding RNAs. In the nucleus, La binds primarily to 3' oligoU containing RNAs, while in the cytoplasm La interacts with an array of different mRNAs lacking a 3' UUU(OH) trailer. An example of the latter is the binding of La to the IRES domain...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkr890
更新日期：2012-02-01 00:00:00
abstract：:Digital PCR provides high sensitivity and unprecedented accuracy in DNA quantification, but current approaches require dedicated instrumentation and have limited opportunities for multiplexing. Here, we present an isothermal platform for digital enumeration of DNA reaction products in multiplex via standard fluorescen...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkaa419
更新日期：2020-07-27 00:00:00
